Merge branch 'hpc-improv' of github.com:Edward-RSE/python into hpc-im…

…prov
sirocco-rt · Feb 9, 2024 · dbbd3e5 · dbbd3e5
2 parents 26ef349 + b90e0cf
commit dbbd3e5
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -1,5 +1,4 @@
-name: C/C++ CI
-
+name: "Python: continuous integration tests"
 on:
   push:
     branches:
@@ -11,64 +10,47 @@ on:
       - "main"
 env:
   PYTHON: ${{ github.workspace }}
-
 jobs:
-  greeting_job:
+  greeting:
+    name: Greeting job
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
     - name: "Print out environment variables"
       run: |
-        echo "WORKSPACE IS $GITHUB_WORKSPACE $PYTHON"
-        $PYTHON/bin/Setup_Py_Dir
+        echo "WORKSPACE IS $GITHUB_WORKSPACE"
+        echo "PYTHON ENV VARIABLE IS: $PYTHON"
 
-  build:
+  build_and_test:
+    name: Build Python and run tests
     runs-on: ubuntu-latest
+    needs: greeting
     steps:
     - uses: actions/checkout@v3
-    - name: configure
+    #- name: "Installing build dependencies"
+    #  run: sudo apt update && apt install -y build-essential cmake
+
+    - name: Configuring Python
       run: ./configure
-    - name: make gh_workflow_install
+    - name: Build GH Workflow version of Python
       run: make gh_workflow_install
 
-  run:
-    runs-on: ubuntu-latest
-    needs: build
-    steps:
-    - uses: actions/checkout@v3
     - uses: actions/setup-python@v3
       with:
         python-version: '3.x' # Version range
-
-    - name: Install dependencies
+    - name: Install Python (the language) dependencies
       run: |
         python -m pip install --upgrade pip
         pip install wheel
         cd $PYTHON/examples/gh-workflow/
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
-    - name: Run unit test framework
-      run: |
-        cd $PYTHON/source/tests
-        make clean
-        make check CC=gcc
+#    - name: Compile programs, again
+#      run: |
+#        cd $PYTHON/source
+#        make CC=gcc INDENT=no all
 
-    - name: compile helper programs and setup
-      run: |
-        cd $PYTHON/source/
-        make clean
-        make CC=gcc INDENT=no all
-        make clean
-        cd $PYTHON/examples/gh-workflow/
-        $PYTHON/bin/Setup_Py_Dir
-
-    - name: balmer test
-      run: |
-        cd $PYTHON/examples/gh-workflow/
-        $PYTHON/bin/py -f -v 1 balmer_test
-        python $PYTHON/py_progs/balmer_decrement.py balmer_test
-
-    - name: read in parameter files
+    - name: Checking Python compiled and can read in inputs correctly
       run: |
         cd $PYTHON/examples/gh-workflow/
         $PYTHON/bin/Setup_Py_Dir
@@ -82,3 +64,14 @@ jobs:
         $PYTHON/bin/py -i ngc5548
         $PYTHON/bin/py -i lamp_post
         $PYTHON/bin/py -i cv_standard_import
+
+    - name: Running unit tests
+      run: |
+        cd $PYTHON/source/tests
+        make check CC=gcc
+
+    - name: Running Balmer test case
+      run: |
+        cd $PYTHON/examples/gh-workflow/
+        $PYTHON/bin/py -f -v 1 balmer_test
+        python $PYTHON/py_progs/balmer_decrement.py balmer_test
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -16,6 +16,7 @@ project(Python LANGUAGES C)
 
 set(CMAKE_C_STANDARD 99)
 set(CMAKE_C_COMPILER mpicc)
+set(CMAKE_CXX_COMPILER mpixx)
 include_directories(include)
 link_directories(lib)
 add_definitions(-DMPI_ON)
@@ -178,21 +179,23 @@ set(PYTHON_SOURCE
     source/communicate_wind.c
     source/communicate_plasma.c
     source/communicate_macro.c
+    source/communicate_spectra.c
 )
 
-
-
 set(PY_WIND_SOURCE source/py_wind_ion.c source/py_wind_macro.c
                    source/py_wind_sub.c source/py_wind_write.c
         source/define_wind.c
-        source/communicate_wind.c)
+        source/communicate_wind.c
+        source/communicate_spectra.c)
 
 set(WINDSAVE2TABLE_SOURCE source/windsave2table_sub.c
         source/define_wind.c
         source/communicate_wind.c)
 
 set(RAD_HYDRO_SOURCE source/rad_hydro_files.c)
 
+set(MODIFY_WIND_SOURCE source/modify_wind.c)
+
 set(INSPECT_WIND_SOURCE source/inspect_wind.c)
 
 set(OPTICAL_DEPTH_SOURCE
@@ -206,16 +209,15 @@ set(TEST_SOURCE
     ${PYTHON_SOURCE}
         source/define_wind.c
         source/tests/tests/test_define_wind.c
-        source/communicate_wind.c)
-
-#${CUDA_SOURCE})
-
+        source/communicate_wind.c
+        source/tests/unit_test_model.c
+        source/tests/tests/test_run_mode.c
+)
 
 # Create the executables for each program, and link the required libraries
 
 # Python
-add_executable(python source/python.c ${PYTHON_SOURCE}
-        source/janitor.c)
+add_executable(python source/python.c ${PYTHON_SOURCE})
 target_link_libraries(python gsl gslcblas m)
 
 # Py_wind
@@ -227,6 +229,22 @@ add_executable(windsave2table source/windsave2table.c ${PYTHON_SOURCE}
                               ${WINDSAVE2TABLE_SOURCE})
 target_link_libraries(windsave2table gsl gslcblas m)
 
+# rad_hydro_files
+add_executable(rad_hydro_files ${PYTHON_SOURCE} ${RAD_HYDRO_SOURCE})
+target_link_libraries(rad_hydro_files gsl gslcblas m)
+
+# modify_wind
+add_executable(modify_wind ${PYTHON_SOURCE} ${MODIFY_WIND_SOURCE})
+target_link_libraries(modify_wind gsl gslcblas m)
+
+# inspect_wind
+add_executable(inspect_wind ${PYTHON_SOURCE} ${INSPECT_WIND_SOURCE})
+target_link_libraries(inspect_wind gsl gslcblas m)
+
+# py_optd
+add_executable(py_optd ${PYTHON_SOURCE} ${OPTICAL_DEPTH_SOURCE})
+target_link_libraries(py_optd gsl gslcblas m)
+
 # test
 add_executable(py_unit_test ${TEST_SOURCE})
 target_link_libraries(py_unit_test m gsl gslcblas cunit)
diff --git a/docs/sphinx/source/input/parameters/Disk/Disk.colour_correction.rst b/docs/sphinx/source/input/parameters/Disk/Disk.colour_correction.rst
@@ -0,0 +1,22 @@
+Disk.colour_correction
+==========================
+Type of colour correction to use
+
+Type
+  Enumerator
+
+Values
+  Done12
+    Temperature dependent form of colour correction from Done 2012 (see :doc:`Disk <../radiation/disk>`)
+
+
+File
+  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+
+
+Parent(s)
+  * :ref:`Disk.radiation`: ``True``
+
+  * :ref:`Disk.type`: ``flat``, ``vertically.extended``
+
+  * :ref:`Disk.rad_type_to_make_wind`: ``bb``, ``models``, ``mod_bb``
diff --git a/docs/sphinx/source/input/parameters/Disk/Disk.rad_type_in_final_spectrum.rst b/docs/sphinx/source/input/parameters/Disk/Disk.rad_type_in_final_spectrum.rst
@@ -7,13 +7,13 @@ Type
 
 Values
   bb
-    Multi-line description, must keep indentation.
+    Blackbody from each annulus
 
   models
-    Multi-line description, must keep indentation.
+    Use model files such as stellar atmosphers
 
-  uniform
-    Multi-line description, must keep indentation.
+  mod_bb
+    modified blackbody (colour correction)
 
 
 File

diff --git a/docs/sphinx/source/input/parameters/Disk/Disk.rad_type_to_make_wind.rst b/docs/sphinx/source/input/parameters/Disk/Disk.rad_type_to_make_wind.rst
@@ -7,10 +7,13 @@ Type
 
 Values
   bb
-    Multi-line description, must keep indentation.
+    Blackbody from each annulus
 
   models
-    Multi-line description, must keep indentation.
+    Use model files such as stellar atmosphers
+
+  mod_bb
+  	modified blackbody (colour correction)
 
 
 File
@@ -26,3 +29,5 @@ Parent(s)
 Child(ren)
   * :ref:`Input_spectra.model_file`
 
+  * :ref:`Disk.colour_correction`
+
diff --git a/docs/sphinx/source/radiation/disk.rst b/docs/sphinx/source/radiation/disk.rst
@@ -1,24 +1,33 @@
 The Disk
 ########
 
-The disk is normally treated as infinitely thin and defined by an inner boundary and an outer boundary.  It assumed to be in  Keplerian  rotation about 
-the central object in the system.   The temperature distribution of the disk
-is normally assumed to be that of a standard Shakura-Sunyaev disk, with a hard
-boundary at its inner edge.   Options are provided for reading in a non-standard
-temperature distribution.
+The disk is normally treated as infinitely thin and defined by an inner boundary and an outer boundary.  It assumed to be in  Keplerian  rotation about the central object in the system.   The temperature distribution of the disk is normally assumed to be that of a standard Shakura-Sunyaev disk, with a hard boundary at its inner edge. Options are provided for reading in a non-standard temperature distribution.
 
 An option is provide for a vertically extended disk, whose thickness increases
-as with distance from the central object object.   
+as with distance from the  central object object.   
 
 The parameters involved in describing a flat disk are::
 
     Disk.type(none,flat,vertically.extended)                 flat
     Disk.radiation(yes,no)                          yes
-    Disk.rad_type_to_make_wind(bb,models)                   bb
+    Disk.rad_type_to_make_wind(bb,models,mod_bb)                   bb
     Disk.temperature.profile(standard,readin)             standard
     Disk.mdot(msol/yr)                         5
     Disk.radmax(cm)                            1e17
 
+Colour Correction (mod_bb)
+=============================
+
+A simple form of the disc colour correction is available in the code, accessible via the 
+:ref:`Disk.rad_type_to_make_wind(bb,models,mod_bb)` keyword. The colour correction factor, :math:`f_{\rm col}`, is defined such that 
+
+.. math::
+    B_\nu (\nu, T) \to f_{\rm col}^{-4} B_\nu (\nu, f_{\rm col} T). 
+
+This correction is designed to approximate the effect of radiative transfer in the disc atmosphere. We adopt the form given by `Done et al. 2012 <https://academic.oup.com/mnras/article/420/3/1848/977649>`_, in which :math:`f_{\rm col}=1` for :math:`T<3\times10^4~{\rm K}`, and for :math:`T>3\times10^4~{\rm K}`
+
+.. math::
+    f_{\rm col}(T)=\left(\frac{T}{3\times10^4~{\rm K}} \right)^{0.82}.
 
 
 Vertically Extended disk (Details)
@@ -52,16 +61,9 @@ not take into account the fact that the disk area of a vertically extended disk
 Non-Standard Temperature Profile
 ================================================
 
-If desired the user can read the temperature profile for the disk from a file. Each
-line in the file should consist of a radius and a temperature (and optionally a value of log g)
-separated by whitespace (in the
-first two columns)  The values are assumed to be entered in a logical order, that is in 
-ascending values of radius. Lines, such as comments or header names of an astropy table, will be ignored.
+If desired the user can read the temperature profile for the disk from a file. Each line in the file should consist of a radius (in cm) and a temperature (in K), and optionally a value of :math:`\log g`. The values separated by whitespace (in the first two columns). The values are assumed to be entered in a logical order, that is in  ascending values of radius. Lines such as comments or header names of an astropy table, will be ignored.
 
-The log g value is not required to generate BB spectra, but is required if the spectrum from the disk is to be generated from a 
-two-dimensional grid of models, usually a set of spectra generated to represent the spectra from a set of stellar 
-atmospheres calculations.  
+The :math:`\log g` value is not required to generate BB spectra, but is required if the spectrum from the disk is to be generated from a two-dimensional grid of models, usually a set of spectra generated to represent the spectra from a set of stellar atmospheres calculations.  
 
-With this option, the radius of the disk will be set to the maximum radius (the last value of r) in 
-the file.  
+With this option, the radius of the disk will be set to the maximum radius (the last value of r) in  the file.